Gene detail

Detailed information of g396.t1 in Calvadosia cruxmelitensis

Genomic Location: not available for this species
NR annotation: MBU2512424.1, fumarate reductase/succinate dehydrogenase flavoprotein subunit [bacterium]
Species Calvadosia cruxmelitensis · all data for this species · gene families

Sequence

Sequence data are not available for Calvadosia cruxmelitensis.
Nucleotide and protein sequences are provided for the species whose genome annotation is complete (see annotated genomes); for this species only the assembly is archived. The functional annotation below is likewise unavailable.

UniProt (Swiss-Prot top hit)

UniProt accession	Description
P08065	Succinate dehydrogenase flavoprotein subunit OS=Bacillus subtilis (strain 168) OX=224308 GN=sdhA PE=1 SV=4
P44894	Fumarate reductase flavoprotein subunit OS=Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd) OX=71421 GN=frdA PE=3 SV=1
V3TQ67	Fumarate reductase flavoprotein subunit OS=Serratia sp. (strain ATCC 39006) OX=104623 GN=frdA PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0000009 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0000059 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0000126 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0000188 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0000220 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0000434 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0000679 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0006259 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0011760 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0014158 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0018555 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0061669 (this species only) · gene tree & orthology
Transcription factor family	THAP · all TF in this species
Transcription factor family	RXR-like · all TF in this species
Transcription factor family	SF-like · all TF in this species
Transcription factor family	GCNF-like · all TF in this species

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF13613 all species →	HTH_Tnp_4	Helix-turn-helix of DDE superfamily endonuclease	Domain	Interproscan
PF05485 all species →	THAP	THAP domain	Domain	Interproscan
PF13359 all species →	DDE_Tnp_4	DDE superfamily endonuclease	Domain	Interproscan
PF08647 all species →	BRE1	BRE1 E3 ubiquitin ligase	Coiled-coil	Interproscan
PF00535 all species →	Glycos_transf_2	Glycosyl transferase family 2	Family	Interproscan
PF20499 all species →	DUF6729	Domain of unknown function (DUF6729)	Domain	Interproscan
PF00104 all species →	Hormone_recep	Ligand-binding domain of nuclear hormone receptor	Domain	Interproscan
PF00105 all species →	zf-C4	Zinc finger, C4 type (two domains)	Domain	Interproscan
PF21788 all species →	TNP-like_GBD	TNP-like, GTP-binding insertion domain	Domain	Interproscan
PF02910 all species →	Succ_DH_flav_C	Fumarate reductase flavoprotein C-term	Domain	Interproscan
PF00890 all species →	FAD_binding_2	FAD binding domain	Family	Interproscan
PF00538 all species →	Linker_histone	linker histone H1 and H5 family	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR027805 all species →	Domain	Transposase, Helix-turn-helix domain	Interproscan
IPR006612 all species →	Domain	THAP-type zinc finger	Interproscan
IPR027806 all species →	Domain	Harbinger transposase-derived nuclease domain	Interproscan
IPR037386 all species →	Family	Coiled-coil domain-containing protein 40	Interproscan
IPR029044 all species →	Homologous_superfamily	Nucleotide-diphospho-sugar transferases	Interproscan
IPR001173 all species →	Domain	Glycosyltransferase 2-like	Interproscan
IPR046616 all species →	Domain	Domain of unknown function DUF6729	Interproscan
IPR035500 all species →	Homologous_superfamily	Nuclear hormone receptor-like domain superfamily	Interproscan
IPR000536 all species →	Domain	Nuclear hormone receptor, ligand-binding domain	Interproscan
IPR001628 all species →	Domain	Zinc finger, nuclear hormone receptor-type	Interproscan
IPR001723 all species →	Family	Nuclear hormone receptor	Interproscan
IPR013088 all species →	Homologous_superfamily	Zinc finger, NHR/GATA-type	Interproscan
IPR050274 all species →	Family	Nuclear hormone receptor family NR2 subfamily	Interproscan
IPR048366 all species →	Domain	Transposable element P transposase-like, GTP-binding insertion domain	Interproscan
IPR036188 all species →	Homologous_superfamily	FAD/NAD(P)-binding domain superfamily	Interproscan
IPR030664 all species →	Family	FAD-dependent oxidoreductase SdhA/FrdA/AprA	Interproscan
IPR015939 all species →	Domain	Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal	Interproscan
IPR003953 all species →	Domain	FAD-dependent oxidoreductase 2, FAD binding domain	Interproscan
IPR011280 all species →	Family	Succinate dehydrogenase/fumarate reductase flavoprotein subunit, low-GC Gram-positive bacteria	Interproscan
IPR027477 all species →	Homologous_superfamily	Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain superfamily	Interproscan
IPR037099 all species →	Homologous_superfamily	Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal domain superfamily	Interproscan
IPR001584 all species →	Domain	Integrase, catalytic core	Interproscan
IPR012337 all species →	Homologous_superfamily	Ribonuclease H-like superfamily	Interproscan
IPR036397 all species →	Homologous_superfamily	Ribonuclease H superfamily	Interproscan
IPR005818 all species →	Domain	Linker histone H1/H5, domain H15	Interproscan
IPR005819 all species →	Family	Linker histone H1/H5	Interproscan
IPR036388 all species →	Homologous_superfamily	Winged helix-like DNA-binding domain superfamily	Interproscan
IPR036390 all species →	Homologous_superfamily	Winged helix DNA-binding domain superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR23080 all species →	THAP DOMAIN PROTEIN	Interproscan
PTHR16275 all species →	COILED-COIL DOMAIN-CONTAINING PROTEIN 40	Interproscan
PTHR22916 all species →	GLYCOSYLTRANSFERASE	Interproscan
PTHR24401 all species →	SI:CH211-243P7.3-RELATED	Interproscan
PTHR24083 all species →	NUCLEAR HORMONE RECEPTOR	Interproscan
PTHR11632 all species →	SUCCINATE DEHYDROGENASE 2 FLAVOPROTEIN SUBUNIT	Interproscan
PTHR33244 all species →	INTEGRASE CATALYTIC DOMAIN-CONTAINING PROTEIN-RELATED	Interproscan
PTHR11467 all species →	HISTONE H1	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005737 all species →	Cellular Component	cytoplasm	Interproscan
GO:0035082 all species →	Biological Process	axoneme assembly	Interproscan
GO:0003700 all species →	Molecular Function	DNA-binding transcription factor activity	Interproscan
GO:0006355 all species →	Biological Process	regulation of DNA-templated transcription	Interproscan
GO:0008270 all species →	Molecular Function	zinc ion binding	Interproscan
GO:0043565 all species →	Molecular Function	sequence-specific DNA binding	Interproscan
GO:0000978 all species →	Molecular Function	RNA polymerase II cis-regulatory region sequence-specific DNA binding	Interproscan
GO:0004879 all species →	Molecular Function	nuclear receptor activity	Interproscan
GO:0006357 all species →	Biological Process	regulation of transcription by RNA polymerase II	Interproscan
GO:0030154 all species →	Biological Process	cell differentiation	Interproscan
GO:0048856 all species →	Biological Process	anatomical structure development	Interproscan
GO:0000104 all species →	Molecular Function	succinate dehydrogenase activity	Interproscan
GO:0005886 all species →	Cellular Component	plasma membrane	Interproscan
GO:0009055 all species →	Molecular Function	electron transfer activity	Interproscan
GO:0009061 all species →	Biological Process	anaerobic respiration	Interproscan
GO:0050660 all species →	Molecular Function	flavin adenine dinucleotide binding	Interproscan
GO:0016491 all species →	Molecular Function	oxidoreductase activity	Interproscan
GO:0015074 all species →	Biological Process	DNA integration	Interproscan
GO:0003676 all species →	Molecular Function	nucleic acid binding	Interproscan
GO:0000786 all species →	Cellular Component	nucleosome	Interproscan
GO:0003677 all species →	Molecular Function	DNA binding	Interproscan
GO:0006334 all species →	Biological Process	nucleosome assembly	Interproscan
GO:0030527 all species →	Molecular Function	structural constituent of chromatin	Interproscan
GO:0003690 all species →	Molecular Function	double-stranded DNA binding	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0030261 all species →	Biological Process	chromosome condensation	Interproscan
GO:0031492 all species →	Molecular Function	nucleosomal DNA binding	Interproscan
GO:0045910 all species →	Biological Process	negative regulation of DNA recombination	Interproscan

Search by domain instead of by gene. Any accession above (InterPro, Pfam, PANTHER, GO, KEGG) can be used as a query on the Functional Domain Search page, which searches all 148 annotated genomes at once.

KEGG pathway

KO	Enzyme	Enzyme ID	Pathway	Map ID	Source
K00239	sdhA, frdA; succinate dehydrogenase flavoprotein subunit	EC:1.3.5.1	Legionellosis	ko05134	deepkoala
K11275	H1_5; histone H1/5	-	Chromosome and associated proteins	ko03036	deepkoala

Searching by KO or pathway ID across all species is available on the KEGG Pathway page.

Co-expression network

Genes whose expression across the transcriptome samples of Calvadosia cruxmelitensis tracks this one. Counts are over the whole network; the network view itself draws at most 100 partners per query gene (CNIDO_NET_TOP_K), so a hub gene can show fewer edges than the number below.

No co-expression network has been built for this species, so this gene has no partners to show. Networks are available for the species listed on the Network Analysis page.

Single-cell expression

Whether this gene can be visualised in the single-cell atlases of Calvadosia cruxmelitensis, and in which cell types it is a marker. Expression is stored per cell, so the violin plot and the cell-type means are computed in the viewer — open a dataset to see them.

No single-cell dataset has been published for this species. The atlases that do exist are listed in the Cell Atlas.

Epigenetic marks

Chromatin and DNA-methylation data covering this gene. Peak calls are listed per sample with the genomic region the peak falls in; DNA methylation is listed as sample availability only, because those tables are queried by the DNA Methylation page itself.

No epigenomic data has been deposited for this species. The assays that exist across the site are described in the Epigenomic Data module.

What you can do with this gene

Every tool below opens with this gene already entered, so you land on the analysis rather than on an empty form. Links open in a new tab.

Analysis	What it does	Status
Primer design	Design PCR / qPCR primers on this gene’s sequence with the published primer3 settings. Opens with the primers already computed.	sequence table not available	–
BLAST	Search this gene’s sequence against the CnidoSite BLAST databases. The query is filled in and the species’ database is preselected — press Run to start.	sequence table not available	–
Expression heatmap	Draw this gene’s expression as a heatmap across all RNA-seq samples, and compare it with the genes you add next to it.	no expression matrix	–
Gene family / orthogroup	Look this gene up in the single-copy orthogroups built from the high-quality cnidarian genomes, and see which other species carry an orthologue.		open →
Gene set analysis	Start a gene-set enrichment analysis with this gene as the seed list. Add more genes on that page before running it.		open →